Exciton circular dichroism couplet arising from nitrile-derivatized aromatic residues as a structural probe of proteins

On the Role of a Conserved Tryptophan in the Chromophore Pocket of Cyanobacteriochrome

The cyanobacteriochrome Slr1393 can be photoconverted between a red (Pr) and green absorbing form (Pg). The recently determined crystal structures of both states suggest a major movement of Trp496 from a stacking interaction with ring D of the phycocyanobilin (PCB) chromophore in Pr to a position outside the chromophore pocket in Pg. Here, we investigated the role of this amino acid during photoconversion in solution using engineered protein variants in which Trp496 was substituted by natural and non-natural amino acids. These variants and the native protein were studied by various spectroscopic techniques (UV-vis absorption, fluorescence, IR, NIR and UV resonance Raman) complemented by theoretical approaches. Trp496 is shown to affect the electronic transition of PCB and to be essential for the thermal equilibrium between Pr and an intermediate state O600. However, Trp496 is not required to stabilize the tilted orientation of ring D in Pr, and does not play a role in the secondary structure changes of Slr1393 during the Pr/Pg transition. The present results confirm the re-orientation of Trp496 upon Pr → Pg conversion, but do not provide evidence of a major change in the microenvironment of this residue. Structural models indicate the penetration of water molecules into the chromophore pocket in both Pr and Pg states and thus water-Trp contacts, which can readily account for the subtle spectral changes between Pr and Pg. Thus, we conclude that reorientation of Trp496 during the Pr-to-Pg photoconversion in solution is not associated with a major change in the dielectric environment in the two states.

An Engineered β-Hairpin Peptide Forming Thermostable Complexes with ZnII , NiII , and CuII through a His3 Site

The three-dimensional structure of a peptide, which determines its function, can denature at elevated temperatures, in the presence of chaotropic reagents, or in organic solvents. These factors limit the applicability of peptides. Herein, we present an engineered β-hairpin peptide containing a His₃ site that forms complexes with Zn^II , Ni^II , and Cu^II . Circular dichroism spectroscopy shows that the peptide-metal complexes exhibit melting temperatures up to 80 °C and remain folded in 6 M guanidine hydrochloride as well as in organic solvents. Intrinsic fluorescence titration experiments were used to determine the dissociation constants of metal binding in the nano- to sub-nanomolar range. The coordination geometry of the peptide-Cu^II complex was studied by EPR spectroscopy, and a distorted square planar coordination geometry with weak interactions to axial ligands was revealed. Due to their impressive stability, the presented peptide-metal complexes open up interesting fields of application, such as the development of a new class of peptide-metal catalysts for stereoselective organic synthesis or the directed design of extremophilic β-sheet peptides.

Site-Specific Interrogation of Protein Structure and Stability

To execute their function or activity, proteins need to possess variability in local electrostatic environment, solvent accessibility, structure, and stability. However, assessing any protein property in a site-specific manner is not easy since native spectroscopic signals often lack the needed specificity. One strategy that overcomes this limitation is to use unnatural amino acids that exhibit distinct spectroscopic features. In this chapter, we describe several such unnatural amino acids (UAAs) and their respective applications in site-specific interrogation of protein structure and stability using standard biophysical methods, including circular dichroism (CD), infrared (IR), and fluorescence spectroscopies.

Probing Intermolecular Interactions of Amyloidogenic Fragments of SOD1 by Site-Specific Tryptophan and Its Noncanonical Derivative

Transient amyloid intermediates are likely to be cytotoxic and play an essential role in amyloid-associated neurodegenerative diseases. Characterization of their structural and dynamic evolution is the key to elucidating the molecular mechanism of amyloid formation. Here, combining circular dichroism (CD), exciton couplet theory, and Fourier transform infrared spectroscopy with site-specific tryptophan (Trp) and its noncanonical derivative 5-cyano-tryptochan (Trp_5CN), we developed a method to monitor strand-to-strand tertiary and sheet-to-sheet quaternary interactions in the aggregation cascades of an amyloidogenic fragment from protein SOD1_28-38 (with the sequence KVKVWGSIKGL). We found that the exciton couplet generated from the B_b band of Trp can be used as a probe for side chain interactions. Its sensitivity can be further improved by four times with the incorporation of Trp_5CN. We further observed a red-shift of ∼2 cm^-1 and a broadening of ∼2 cm^-1 in the IR band generated from the CN stretch during the aggregation, which we attributed to the transition from a corkscrew-like structure to a cross-linked intermediate phase. We show here that the integration of optical methods with unique aromatic side chain-related probes is able to elucidate amyloid intermolecular interactions and even capture elusive transient intermediates on and off the amyloid assembling pathway.

Folding and Unfolding of the Tryptophan Zipper in the Presence of Two Thioamide Substitutions

We studied the stability and folding and unfolding kinetics of the tryptophan zipper, containing different double thioamide subsitutions. Conformation change was triggered by photoisomerization of an integrated AMPP photoswitch in the turn region of the hairpin, and transient spectra were recorded in the deep UV and the mid-IR, covering the time window of the (un)folding transition from picoseconds to tens of microseconds. Thio-substitution of inward-pointing backbone carbonyls was found to strongly destabilize the β-hairpin structures, whereas molecules with two outward pointing thio-carbonyls showed similar or enhanced stability with respect to the unsubstituted sequence, which we attribute to stronger interstrand hydrogen bonding. Thiolation of the two Trp residues closest to the turn can even prevent the opening of the hairpin after cis-trans isomerization of the switch. The circular dichroism due to the two thioamide ππ* transitions is spectrally well-separated from the aromatic tryptophan signal. It changes upon photoswitching, reflecting a local change in coupling and geometry.

Secondary Structure of the Novel Myosin Binding Domain WYR and Implications within Myosin Structure

Structural changes in the myosin II light meromyosin (LMM) that influence thick filament mechanical properties and muscle function are modulated by LMM-binding proteins. Flightin is an LMM-binding protein indispensable for the function of Drosophila indirect flight muscle (IFM). Flightin has a three-domain structure that includes WYR, a novel 52 aa domain conserved throughout Pancrustacea. In this study, we (i) test the hypothesis that WYR binds the LMM, (ii) characterize the secondary structure of WYR, and (iii) examine the structural impact WYR has on the LMM. Circular dichroism at 260-190 nm reveals a structural profile for WYR and supports an interaction between WYR and LMM. A WYR-LMM interaction is supported by co-sedimentation with a stoichiometry of ~2.4:1. The WYR-LMM interaction results in an overall increased coiled-coil content, while curtailing ɑ helical content. WYR is found to be composed of 15% turns, 31% antiparallel β, and 48% 'other' content. We propose a structural model of WYR consisting of an antiparallel β hairpin between Q92-K114 centered on an ASX or β turn around N102, with a G1 bulge at G117. The Drosophila LMM segment used, V1346-I1941, encompassing conserved skip residues 2-4, is found to possess a traditional helical profile but is interpreted as having <30% helical content by multiple methods of deconvolution. This low helicity may be affiliated with the dynamic behavior of the structure in solution or the inclusion of a known non-helical region in the C-terminus. Our results support the hypothesis that WYR binds the LMM and that this interaction brings about structural changes in the coiled-coil. These studies implicate flightin, via the WYR domain, for distinct shifts in LMM secondary structure that could influence the structural properties and stabilization of the thick filament, scaling to modulation of whole muscle function.

Self-assembly of virulent amyloid-derived peptides into nanoantibacterials

Current strategies for the design of antibacterial peptides show limitations in the development of assembled antibacterial peptides due to the challenges in simultaneously balancing the antibacterial activity and assembling behavior. Herein, we report on one strategy for the design of antibacterial peptides derived from virulent amyloids and investigate their self-assembly into nanostructures with remarkable antibacterial activity. The peptides were either directly truncated from virulent amyloid peptide PSM α3 or mutated from the original sequence by replacing the lysine and phenylalanine residues with arginine or tryptophan, leading to three undecapeptides. Conformational and morphological results indicated the formation of nanotubes and twisted nanoribbons by the truncated peptide and the mutated peptide, respectively, predominately driven by anti-parallel β-sheets. Bacterial culturing experiments revealed that the two mutated peptides possessed remarkable antibacterial activity against both Gram-positive and Gram-negative bacteria by disrupting the bacterial membrane at a concentration above their critical aggregation concentrations, thus leading to two nanoantibacterials. Our findings demonstrate that biomimetic peptides originated from virulent amyloids exhibit great potential in the development of assembled antibacterial peptides, thus providing a new strategy for simultaneously addressing the antibacterial activity and pharmacokinetics of natural antibacterial peptides in the future.

Can glycine betaine denature proteins?

Glycine betaine (GB) is a naturally occurring osmolyte that has been widely recognized as a protein protectant. Since GB consists of a methylated ammonium moiety, it can engage in strong cation-π interactions with aromatic amino acid sidechains. We hypothesize that such specific binding interactions would allow GB to decrease the stability of proteins that are predominantly stabilized by a cluster of aromatic amino acids. To test this hypothesis, we investigate the effect of GB on the stability of two β-hairpins (or mini-proteins) that contain such a cluster. We find that for both systems the stability of the folded state first decreases and then increases with increasing GB concentration. Such non-monotonic dependence not only confirms that GB can act as a protein denaturant, but also underscores the complex interplay between GB's stabilizing and destabilizing forces toward a given protein. While stabilizing osmolytes all have the tendency to be excluded from the protein surface which is the action underlying their stabilizing effect, our results suggest that in order to quantitatively assess the effect of GB on the stability of any given protein, specific cation-π binding interactions need to be explicitly considered. Moreover, our results show, consistent with other studies, that cation methylation can strengthen the respective cation-π interactions. Taken together, these findings provide new insight into the mechanism by which amino acid-based osmolytes interact with proteins.

Microscopic Insight into the Protein Denaturation Action of Urea and Its Methyl Derivatives

We employ site-specific, linear and nonlinear infrared spectroscopic techniques as well as fluorescence spectroscopy and molecular dynamics simulations to investigate the binding interactions of urea and three of its derivatives, methylurea, 1,3-dimethylurea, and tetramethylurea, with protein aromatic and polar side chains. We find that (1) urea methylation leads to preferential interactions between the cosolvent molecules and aromatic side chains with an affinity that increases with the number of methyl groups; (2) interactions with tetramethylurea cause significant dehydration of aromatic side chains and the effect is most pronounced for tryptophan; and (3) while neither urea nor tetramethylurea shows preferential accumulation around a polar side chain, the number of hydrogen-bond donors around this side chain is significantly decreased in the presence of tetramethylurea. Taken together, our findings suggest that these urea derivatives, especially tetramethylurea, can effectively disrupt hydrophobic interactions in proteins. Additionally, tetramethylurea can promote intramolecular hydrogen-bond formation and hence induce α-helix folding in peptides, as observed.

Selective Excitation of Cyanophenylalanine Fluorophores for Multi-Site Binding Studies

Recently, it has been shown that nitrile-derivatized phenylalanines possess distinct fluorescent properties depending on the position of the cyano-group within the aromatic ring. These fluorophores have potential as probes for studying protein dynamics due to their sensitivity to local environment. Herein, we demonstrate that 2-cyanophenylalanine (Phe_2CN) and Phe_4CN can independently monitor multiple sites during the Ca²⁺ dependent binding of a skeletal muscle myosin light chain kinase (MLCK) peptide fragment to the protein calmodulin (CaM). These cyano-probes were incorporated at two different positions along the peptide chain and monitored simultaneously via selective excitation of the two chromophores. The peptide was labeled with Phe_4CN at a residue known to bind to a hydrophobic binding pocket of CaM, while Phe_2CN was designed to acquire dynamics external to the binding pocket. By selectively exciting each of the chromophores, it was determined that the fluorescence emission of Phe_4CN located at position 581 of MLCK was quenched in the presence of CaM, while no significant change in Phe_2CN emission was observed at exposed position 594. The CaM binding affinity (K_d) of the double labeled MLCK peptide was calculated to be approximately 64 nM, which is in agreement with previous measurements. These results indicate that multiple Phe_CN reporters within the same peptide can simultaneously detect variations in the local environment, and that these fluorophores could be utilized to investigate a wide variety of biological problems.

Do guanidinium and tetrapropylammonium ions specifically interact with aromatic amino acid side chains?

Many ions are known to affect the activity, stability, and structural integrity of proteins. Although this effect can be generally attributed to ion-induced changes in forces that govern protein folding, delineating the underlying mechanism of action still remains challenging because it requires assessment of all relevant interactions, such as ion-protein, ion-water, and ion-ion interactions. Herein, we use two unnatural aromatic amino acids and several spectroscopic techniques to examine whether guanidinium chloride, one of the most commonly used protein denaturants, and tetrapropylammonium chloride can specifically interact with aromatic side chains. Our results show that tetrapropylammonium, but not guanidinium, can preferentially accumulate around aromatic residues and that tetrapropylammonium undergoes a transition at ∼1.3 M to form aggregates. We find that similar to ionic micelles, on one hand, such aggregates can disrupt native hydrophobic interactions, and on the other hand, they can promote α-helix formation in certain peptides.

Infrared and fluorescence assessment of the hydration status of the tryptophan gate in the influenza A M2 proton channel

The M2 proton channel of the influenza A virus has been the subject of extensive studies because of its critical role in viral replication. As such, we now know a great deal about its mechanism of action, especially how it selects and conducts protons in an asymmetric fashion. The conductance of this channel is tuned to conduct protons at a relatively low biologically useful rate, which allows acidification of the viral interior of a virus entrapped within an endosome, but not so great as to cause toxicity to the infected host cell prior to packaging of the virus. The dynamic, structural and chemical features that give rise to this tuning are not fully understood. Herein, we use a tryptophan (Trp) analog, 5-cyanotryptophan, and various methods, including linear and nonlinear infrared spectroscopies, static and time-resolved fluorescence techniques, and molecular dynamics simulations, to site-specifically interrogate the structure and hydration dynamics of the Trp41 gate in the transmembrane domain of the M2 proton channel. Our results suggest that the Trp41 sidechain adopts the t90 rotamer, the χ2 dihedral angle of which undergoes an increase of approximately 35° upon changing the pH from 7.4 to 5.0. Furthermore, we find that Trp41 is situated in an environment lacking bulk-like water, and somewhat surprisingly, the water density and dynamics do not show a measurable difference between the high (7.4) and low (5.0) pH states. Since previous studies have shown that upon channel opening water flows into the cavity above the histidine tetrad (His37), the present finding thus provides evidence indicating that the lack of sufficient water molecules near Trp41 needed to establish a continuous hydrogen bonding network poses an additional energetic bottleneck for proton conduction.